Method for detecting West Nile virus nucleic acids in the 5′ non-coding/capsid region

A method of detecting the presence of West Nile virus in a test sample, comprising the steps of:

• (a) performing an in vitro nucleic acid amplification reaction to synthesize an amplicon comprising a West Nile virus nucleic acid sequence, said in vitro nucleic acid amplification reaction comprising extension of a first primer by a DNA polymerizing enzyme to synthesize a first primer extension product using as a template any West Nile virus polynucleotides contained in said test sample,
• wherein said first primer is up to 51 nucleotides in length and comprises a 3′ terminal target-complementary sequence of 20 contiguous bases of SEQ ID NO:16, and
• wherein said West Nile virus nucleic acid sequence of said amplicon terminates at a 5′-end thereof with a sequence selected from the group consisting of SEQ ID Nos:
• 23-28;
• (b) hybridizing to said first primer extension product and to said amplicon an oligonucleotide up to 37 nucleotides in length that comprises 13-37 contiguous bases of SEQ ID NO:95, allowing for RNA and DNA equivalent bases, to form a hybridization product;
• and
• (c) detecting the hybridization product as an indication of the presence of West Nile virus in the test sample.